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Why Does My Toilet Smell Of Urine Despite Cleaning It?

by | Nov 14, 2023 | Toilet Cleaning

No one likes stinky toilets. That’s just the truth. It’s no fun walking inside the bathroom only to get a face full of a nasty smell.

But if you’ve already cleaned and there’s still a urine odour, there could be a problem!

Some reasons why the toilet smells like urine include:

If your toilet always smells like wee, act quickly! And urine luck (ha!) since we’ve put together the most common causes for a pee smell in your bathroom and how to fix it.


Why The Toilet Smells of Urine Despite Cleaning

If you notice that your toilet smells even after cleaning, there could be a few reasons! 

Fortunately, the most common causes have straightforward fixes.


1. Lack of flushing

First things first, check the toilet! It’s possible your bathroom smells like urine because someone forgot to flush.

While it’s encouraged not to flush every time to conserve water, you shouldn’t leave the dunny unflushed too long either. Otherwise, the contents of the toilet bowl will create unpleasant odours and urine stains.

It’s important to note that even if a toilet is unused, you should still flush it! The wet, enclosed space is a breeding ground for mould and bacteria. Flushing will help prevent mould or insect larvae.


How to fix it:

Simple – flush the toilet! Then switch on the exhaust fan or open the windows to air out the bathroom and get rid of the urine smell.


2. Overlooked toilet cleaning

When cleaning the toilet, we often focus on the bowl and the exterior. Because of this, there are all sorts of nooks and crannies we might miss.

Urine can get trapped under the toilet seat, along the rim, in the hinges, or even on the bidet. That’ll eventually lead to an unpleasant urine smell.


How to fix it:

Make sure you clean thoroughly whenever you tackle the toilet. A good toilet brush makes a big difference.

Use a disinfectant spray or wipe on the seat, including the hinges, and on the bidet attachment as well.

Alternatively, a thorough house cleaner will cover all the problem areas in toilets.


3. Urine in other bathroom places

Modern toilet bowl in interior of bathroom

This is especially common in homes with kids who are still learning how to use the toilet, or adults with fine motor issues. 

Wee can spray or spill onto other things like:

  • Bath mats or rugs
  • Toilet paper
  • Nearby cabinets
  • Bathroom floor or walls

If it’s not cleaned right away, urine smells will eventually build up.


How to fix it:

Patience and persistence! Clean up any spills ASAP with a mop or some cloths and a disinfectant spray.

Be gentle and encourage your child as they learn. But if an adult is the problem and their motor skills are fine, you’re welcome to give a little stink-eye!


4. Inefficient toilet cleaner

Cleaning supplies and toilet bowl in bathroom

Sometimes the problem isn’t the toilet itself, but the cleaning products you’re using!

It could be that your chosen cleaner isn’t breaking down the organic compounds in the toilet. That will eventually lead to unpleasant urine smells.


How to fix it:

It’s important to choose a toilet cleaner that’ll remove stains and disinfect the bowl. 

The cleaner will also remove urine odour at the same time.


5. Leaking seal

The wax ring or wax seal is the seal between the bottom of the toilet and the sewer pipe. It prevents leaks and odours from escaping.

Wax seals are built to last, but they can still degrade over time. If the seal breaks or peels off the floor, bad smells will start to emanate. Bacteria can also accumulate around the seals.

If you’ve checked absolutely everywhere and nothing seems to work, chances are the toilet wax ring is causing the urine smell.


How to fix it:

Unfortunately, the only way to fix this is to replace the wax ring. It’s located under the toilet base, so you’ll need to detach the toilet completely to access it.

While you’ve got the toilet out of the way, take the opportunity to clean underneath the toilet. These parts are usually inaccessible otherwise.

Use a mix of white vinegar and warm water in a spray bottle, or a bleach-based cleaner.

If you don’t feel confident about removing your toilet, bring in a professional. The last thing you want to do is break your toilet!


6. Dirty toilet tank

toilet tank

This isn’t caused by urine, but the toilet tank can definitely emanate something similar to urine smells.

Bacteria or mould spores can grow in the feeder pipes, especially during hot and humid weather. The dark, moist, and enclosed environment allows them to thrive.

This will eventually lead to an unpleasant bathroom smell. It can also be a health hazard.


How to fix it:

Deep clean your toilet’s cistern twice a year – or once every 3 months if you have a hard water supply. 

But if you notice unpleasant toilet smells, clean the tank ASAP.


7. Broken toilet flange

The toilet wax ring isn’t the only fixture that can cause problems. You may also have a broken or cracked flange.

The flange is the pipe that secures your toilet to the floor and connects the closest to the drain pipe. That means the dirty water passes through this fixture as it drains out of the bowl.

When the flange breaks, it will begin leaking sewer gases, dirty water, and urine smells. You’ll also want to check if it has caused water damage to the floorboards.

Improper installation could also lead to leaks from the flange.


How to fix it:

Much like the wax ring, you’ll need to have the flange replaced. 

This will also involve removing your toilet from the base so you can access the broken fixture.


8. Mould or bacteria

Mineral deposits and urine stains in your toilet can create an environment where mould or bacteria will thrive.

The organisms can come through your pipes and settle under the toilet rim, around the seat, or at the bottom of the bowl. They’ll eventually produce foul smells that can be similar to urine.

You can identify mould issues if you have green or black toilet bowl stains. Meanwhile, pink stains will be a sign of Serratia marcescens bacteria.


How to fix it:

Your best bet to kill off any mould or bacteria is to use bleach! Opt for an oxygen-based bleach product as it’s less reactive than chlorine.

Dilute the bleach according to the packaging instructions. Then use a scrub brush to remove the mould or stains.

Always make sure you’re wearing protective equipment when cleaning with bleach. This includes rubber gloves, a face mask, and some eye protection.


9. Garbage cans

White toilet bowl and metallic trash bin in interior of light bathroom

Sometimes the toilet itself isn’t the cause of the funky bathroom smell. 

Used toilet paper left in the rubbish bin will also eventually create an unpleasant odour.


How to fix it:

Empty the rubbish bin once it’s full – or earlier, if you detect any urine odours. 

There are also rubbish bin deodorisers you can use to prevent any stink!


How to Prevent a Urine Smell in the Toilet

Prevention is better than cure, as they say. 

Some things are out of your control – such as broken fixtures – but you can take steps to prevent the smell of urine from building in your bathroom.


Clean after use

hand cleaning toilet seat by a wet wipe

Make sure family or roommates are mindful of wiping the toilet after use! You can even keep a disinfectant spray or pack of wipes handy.

For kids, encourage them to tell you right away if they’ve had a potty accident. If they’re old enough, you can also teach them basic cleaning skills so they can tidy up after themselves.


Thorough routine cleaning

Don’t scrub the toilet and call it a day! Be thorough every time you clean the dunny, from the toilet seat to the base.

HINT: You’ll also need to clean the toilet brush and holder after every use. You can’t clean with dirty tools!


Toilet or tank cleaners

There are products you can use to maintain toilet hygiene in between cleaning.

Try an in-tank toilet cleaner that acts on the water inside the cistern. Or you can use a product in the bowl, such as the Bref Blue Active or Duck Fresh Discs.


How to Remove Bathroom Smells

Besides the toilet, you can keep your bathroom smelling fresh in several ways. 

And that’s good not just for your nose, but for hygiene as well!


Install a deodoriser

cleaning toilet bowl

There are lots of types available! Bathroom deodorisers can come as gel, plug-ins, sachets/pouches, or spray dispensers.

Simply choose your favourite type and scent, and place it inside the bathroom to cover up any unpleasant smells.

However, if you or someone living with you has hay fever or similar allergies, this might trigger a reaction.



Make sure your bathroom is properly ventilated! This will go a long way towards dissipating any bathroom smells – not just the ones from the toilet.

Proper ventilation will also prevent mould or mildew from developing.

Keep windows open as much as possible, or the door if it’s an interior space. And of course, switch on the exhaust any time you use the bathroom.


Clean the bathroom regularly

You should clean your bathroom at least once a week for proper maintenance and hygiene. That includes everything from the toilet to the shower stall.

Something people may not know about is that you can have your pipes cleaned! There are services that will clean your pipes and drains. It’s good for your plumbing – and also your peace of mind.

About Author

Sophie Franklin

Sophie is the subject matter expert within Maid2Match. Most importantly though she is our biggest fan girl and generous in sharing what she knows.


About Author

Sophie Franklin

Sophie is the subject matter expert within Maid2Match. Most importantly though she is our biggest fan girl and generous in sharing what she knows.